Sequence specificity for removal of uracil from U·A pairs and U·G mismatches by uracil‐DNA glycosylase from Escherichia coli, and correlation with mutational hotspots

Abstract

The rate of removal of uracil from different positions in double-stranded DNA by uracii-DNA glycosylase from Escherichia coli varied more than 15-fold. Consensus sequences for good and poor removal were 5'-(A/T)UA(A/T)-3' and 5'-(G/ C)U(T/G/C)-3', respectively. In general, the sequence context surrounding U was more important for the rate of removal than whether U was present in U" A pairs or U-G mispairs. Rates of removal of U from sites of amber mutations in the lacl gene, where mutation frequencies and deamination rates were known, indicated that the observed variation in removal is biologically significant.

DNA glycosylases in the base excision repair of DNA

“…The rate differs as much as 20-fold between the ' best ' (A\T\UAA) and ' worst ' (G\CUG\C\T) sequences. Usually, but not always [34], the rate of removal is greater from U\G mispairs than from U :A pairs [35][36][37]. A low removal rate tends to be correlated with the occurrence of ' hot spots ' for mutation [36], similar to the correlation between slow spots for the repair of cyclobutyl dimers and hot spots for mutations [38,39].…”

Uracil in DNA – occurrence, consequences and repair

“…This is also reflected by the different efficiency whereby uracil is excized from different sequence contexts (Eftedal et al, 1993;Nilsen et al, 1995). Recently the sequence specificity was reexamined using both single-stranded and duplex DNA substrates (Bellamy and Baldwin, 2001), and the authors conclude that the observed variations were not due to stability of the uracil itself within the DNA structure.…”

Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme

“…It has been reported that the rate of glycosylase activity associated with repair of a modified nucleobase can be greatly affected by DNA sequence context (28,29). Therefore, we treated the naked uracil-containing DNAs with limiting amounts (0.2 nM) of UDG and APE1 to determine their relative rates of cleavage.…”